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jianchaoyv金蟲 (小有名氣)
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【求助】怎么看力場文件? 已有2人參與
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!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CA 0.000000 -0.070000 1.992400 ! ALLOW ARO ! benzene (JES) CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CD 0.000000 -0.070000 2.000000 ! ALLOW POL ! adm jr. 3/19/92, acetate a.i. and dH of solvation CE1 0.000000 -0.068000 2.090000 ! ! for propene, yin/adm jr., 12/95 CE2 0.000000 -0.064000 2.080000 ! ! for ethene, yin/adm jr., 12/95 CM 0.000000 -0.110000 2.100000 ! ALLOW HEM ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO ! benzene (JES) CS 0.000000 -0.110000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! propane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 CY 0.000000 -0.070000 1.992400 ! ALLOW ARO ! TRP, JWK 08/29/89 ! carbon wildcards, following atom order is essential for accurate results !C* 0.000000 -0.070000 2.000000 !CP% 0.000000 -0.090000 1.800000 !C%1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 !C%2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 !C%3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 !CPH+ 0.000000 -0.050000 1.800000 !C 0.000000 -0.110000 2.000000 !CA 0.000000 -0.070000 1.992400 !CE1 0.000000 -0.068000 2.090000 !CE2 0.000000 -0.064000 2.080000 !CM 0.000000 -0.110000 2.100000 !CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI !CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 !CS 0.000000 -0.110000 2.200000 !CY 0.000000 -0.070000 1.992400 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HE1 0.000000 -0.031000 1.250000 ! ! for propene, yin/adm jr., 12/95 HE2 0.000000 -0.026000 1.260000 ! ! for ethene, yin/adm jr., 12/95 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO ! JES 8/25/89 values from Jorgensen fit to hydration energy HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO ! adm jr., 6/27/90, his HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO ! adm jr., 6/27/90, his HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS 0.000000 -0.100000 0.450000 ! ALLOW SUL ! methanethiol pure solvent, adm jr., 6/22/92 HT 0.000000 -0.046000 0.224500 ! ALLOW WAT !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete ! hydrogen wildcards !H* 0.000000 -0.046000 0.224500 !HA 0.000000 -0.022000 1.320000 !HE1 0.000000 -0.031000 1.250000 !HE2 0.000000 -0.026000 1.260000 !HB 0.000000 -0.022000 1.320000 !HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 !HR1 0.000000 -0.046000 0.900000 !HR2 0.000000 -0.046000 0.700000 !HR3 0.000000 -0.007800 1.468000 !HS 0.000000 -0.100000 0.450000 ! N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 0.000000 -0.200000 1.850000 ! ALLOW POL ! JG 8/27/89; note: NH1 in ARG was changed to NC2. NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH2 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. NP 0.000000 -0.200000 1.850000 ! ALLOW PRO ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NY 0.000000 -0.200000 1.850000 ! ALLOW ARO ! trp, JWK ! nitrogen wildcards !N* 0.000000 -0.200000 1.850000 !N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 !NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid carbonyl O OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) OM 0.000000 -0.120000 1.700000 ! ALLOW HEM ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 9/17/90, avoid O* wildcard OT 0.000000 -0.152100 1.768200 ! ALLOW WAT !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete ! oxygen wildcards !O* 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 !OC 0.000000 -0.120000 1.700000 !OH1 0.000000 -0.152100 1.770000 !OM 0.000000 -0.120000 1.700000 !OS 0.000000 -0.152100 1.770000 !OT 0.000000 -0.152100 1.768200 !CAL 0.000000 -0.120000 1.710000 ! ALLOW ION ! !Calcium (BP) FE 0.010000 0.000000 0.650000 ! ALLOW HEM ! Heme (6-liganded): Iron atom (KK 05/13/91) S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION ! adm jr., 3/3/92, dimethyldisulphide pure solvent SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 ZN 0.000000 -0.250000 1.090000 ! ALLOW ION ! RHS March 18, 1990 DUM 0.000000 -0.000000 0.000000 ! ! dummy atom HE 0.000000 -0.021270 1.4800 ! ! helium, experimental pot. energy surface, adm jr., 12/95 NE 0.000000 -0.086000 1.5300 ! neon, semiempirical pot. energy surface, adm jr., 12/95 !lipids section HOL 0.0 -0.046 0.2245 HAL1 0.0 -0.022 1.3200 ! alkane, 3/92 HAL2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98 HAL3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 HCL 0.0 -0.046 0.2245 ! ethanolamine !HT 0.0 -0.046 0.2245 HL 0.0 -0.046 0.7 ! polar H on NC4+ HEL1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95 HEL2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95 ! CL 0.0 -0.070 2.00 ! methyl acetate update CTL1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92 CTL2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CTL3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CTL5 0.0 -0.0800 2.06 0.0 -0.01 1.9 ! old CTL3 ! maintained for tetramethylammonium CEL1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95 CEL2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95 ! OBL 0.0 -0.12 1.70 0.0 -0.12 1.4 OCL 0.0 -0.12 1.70 O2L 0.0 -0.12 1.70 OHL 0.0 -0.1521 1.77 OSL 0.0 -0.1521 1.77 !OT 0.0 -0.1521 1.7682 ! NH3L 0.0 -0.20 1.85 ! ethanolamine NTL 0.0 -0.20 1.85 ! as all other nitogens ! SL 0.0 -0.47 2.1 ! methylsulfate PL 0.0 -0.585 2.15 ! ADM Jr. !DUM 0.0 -0.00 0.0 ! dummy atom ! ! ions, note lack of NBFIXes ! SOD 0.0 -0.0469 1.36375 ! sodium ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol POT 0.0 -0.0870 1.76375 ! potassium ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol CLA 0.0 -0.150 2.27 ! chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol CAL 0.0 -0.120 1.367 ! Calcium ! S. Marchand and B. Roux, dA = -384.8 kcal/mol MG 0.0 -0.0150 1.18500 ! Magnesium ! B. Roux dA = -441.65 CES 0.0 -0.1900 2.100 ! Cesium, so far untested. 怎樣看力場文件?比如:文獻(xiàn)中碳碳的epsilon=0.086Kcal/mol,碳氧的epsilon=0.114333,在上面給的參數(shù)中碳碳的epsilon是多少?碳氧的epsilon是多少? |
榮譽(yù)版主 (著名寫手)
阿超
金蟲 (著名寫手)
劉蘇州
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這是charmm 力場的文件, top 和par 都有詳細(xì)的注釋, 以!開頭 這里面有你想要的很多信息 !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) 表示每對Eps 的數(shù)值為兩個原子的幾何平均 !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 表示第三項是Eps 的數(shù)值 不清楚你說的C 和O 是什么類型, 舉個羰基C,O的例子 CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION 上面兩行是這兩個原子的, 為什么這兩行是? 這是常識, 入行必須知道 碳碳的epsilon=-sqrt(0.07*0.07), 碳氧的epsilon=-sqrt(0.07*0.12) 不同原子類型的參數(shù)天差地別, 不同力場的參數(shù)也是各自為政 |
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